vera-weili / ops_ase

The project

This project hooks up openpathsampling package with ase molecular dynamics modules. The tutorials show several examples to display the workflow.

Create conda environment

For Mac/Linux, create a conda environment using env_mac_linux.yml:

conda env create -f env_mac_linux.yml

For Windows, openpathsampling is not thoroughly tested and not available from a conda channel, the package needs to be installed by pip. A conda environment can be created by:

conda env create -f env_windows.yml

Jupyter notebook tutorials

First, enable the nglview extension for interactively viewing molecular structures and trajectories:

jupyter-nbextension enable nglview --py --sys-prefix

Start the notebook in terminal:

jupyter notebook